Transportation infrastructure is an important means for local governments to attract investment, but under the condition of open trade, the impact of transportation infrastructure on the location choice of enterprises is heterogeneous. The empirical analysis based on industry subdivision level of the manufacturing industry of China’s prefecture-level cities shows that there is significant boosting effect of local transportation infrastructure construction on the attraction of the enterprises, but this effect has obvious regional and industrial heterogeneity, that compared with other regions and industries, in the regions with high trade openness level, in coastal area, in transportation network center area, for “transportation intensive industries” with high dependence degree on transportation, and for “non-expectation industries with less tax payment and with low efficiency, there is more strong effect of local transportation infrastructure construction on the attraction of the enterprises. In addition, local transportation infrastructure construction and trade openness both can boost the attraction of the enterprises, and the two effects support each other. Local governments should uphold the heterogeneous impact of transportation infrastructure on the location choice of the enterprises, promote the cooperation between transportation infrastructure construction and industrial development, improve business environment and other factors while actively boosting local transportation infrastructure construction, actively integrate local transportation into national transportation system, and rationally lay out local transportation infrastructure construction.